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- PDB-7bz4: The mutant variant of PNGM-1. H279 was substituted for alanine to... -

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Basic information

Entry
Database: PDB / ID: 7bz4
TitleThe mutant variant of PNGM-1. H279 was substituted for alanine to study metal coordination.
ComponentsMetallo-beta-lactamase PNGM-1
KeywordsANTIBIOTIC / RNase Z / MBLs / Zinc binding motif
Function / homology
Function and homology information


3'-tRNA processing endoribonuclease activity / beta-lactamase activity / beta-lactamase / metal ion binding
Similarity search - Function
Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase PNGM-1
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
Model detailsPNGM-1 residue H91 was substituted to Alanine
AuthorsPark, Y.S. / Kang, L.W. / Lee, J.H.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Study of Metal Binding and Coordination in Ancient Metallo-beta-Lactamase PNGM-1 Variants.
Authors: Park, Y.S. / Kim, T.Y. / Park, H. / Lee, J.H. / Nguyen, D.Q. / Hong, M.K. / Lee, S.H. / Kang, L.W.
History
DepositionApr 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase PNGM-1
B: Metallo-beta-lactamase PNGM-1
C: Metallo-beta-lactamase PNGM-1
D: Metallo-beta-lactamase PNGM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7998
Polymers166,5384
Non-polymers2624
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SuperoseTM 12 10/300 was used for the experiment. Buffer composition was 0.05 M Tris-HCl pH 7.0, 150mM NaCl, 3 mM Mercaptoethanol.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28370 Å2
ΔGint-307 kcal/mol
Surface area44960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.857, 82.964, 164.037
Angle α, β, γ (deg.)90.000, 110.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Metallo-beta-lactamase PNGM-1


Mass: 41634.457 Da / Num. of mol.: 4 / Mutation: H279A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U8UYM6, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 7.5
Details: 0.05 M HEPES, 0.15 M Magnesium Acetate, 0.2 M Ammonium Acetate and 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: steady flow of liquid nitrogen was used to maintain 100 K.
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 79596 / % possible obs: 96.8 % / Redundancy: 5 % / CC1/2: 0.977 / CC star: 0.994 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.076 / Rrim(I) all: 0.183 / Rsym value: 0.165 / Χ2: 1.084 / Net I/av σ(I): 9.591 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.16-2.23.70.43738620.7150.2370.50.45395.2
2.2-2.243.90.439530.8020.2120.4550.48495.6
2.24-2.283.90.37538990.8740.1970.4260.48596.3
2.28-2.3340.37439370.8420.1960.4250.50896.6
2.33-2.384.10.37840250.7830.1980.4290.596.7
2.38-2.434.10.34838980.7940.1820.3950.51996.3
2.43-2.494.10.32437590.8040.170.3690.53292.3
2.49-2.564.70.31339830.9010.1530.350.54697
2.56-2.644.90.29140060.9380.1370.3230.61797.6
2.64-2.7250.28139890.9290.1320.3120.64597.4
2.72-2.825.10.25639840.9490.1190.2840.797.4
2.82-2.935.20.23240070.9590.1070.2570.77697.9
2.93-3.065.20.240630.970.0920.2210.89198.2
3.06-3.235.10.17238730.9730.080.191.08394.7
3.23-3.435.80.15340280.9810.0660.1671.28598.1
3.43-3.696.10.13340930.9880.0560.1441.57198.9
3.69-4.066.10.11940710.990.0510.131.76898.9
4.06-4.655.90.10440520.990.0450.1141.99998.1
4.65-5.866.30.09640190.9930.040.1041.89196.8
5.86-506.40.08640950.9920.0360.0942.01696.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→48.08 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.344 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3906 4.9 %RANDOM
Rwork0.1933 ---
obs0.1961 75690 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.1 Å2 / Biso mean: 18.988 Å2 / Biso min: 1.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.16→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11344 0 4 694 12042
Biso mean--17.33 21.51 -
Num. residues----1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311673
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710152
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.63915908
X-RAY DIFFRACTIONr_angle_other_deg1.311.57323484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.53451436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96722.39636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.511151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3211567
X-RAY DIFFRACTIONr_chiral_restr0.0760.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022626
LS refinement shellResolution: 2.16→2.212 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.326 241 -
Rwork0.272 5285 -
obs--91.25 %

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